diff setmetadata.xml @ 0:7499e3a586c0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/setmetadata.xml	Mon Apr 04 10:30:36 2022 +0000
@@ -0,0 +1,91 @@
+<tool id="ampvis2_setmetadata" name="ampvis2 set metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+    <description>types</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="header"/>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$rscript'
+    ]]></command>
+    <configfiles>
+        <configfile name="rscript"><![CDATA[
+            library(lubridate, quietly = TRUE)
+            data <- readRDS("$data")
+            #for col in $numbers
+                data\$metadata\$$col <- as.numeric(data\$metadata\$$col)
+            #end for
+            #for col in $integers
+                data\$metadata\$$col <- as.integer(data\$metadata\$$col)
+            #end for
+            #for col in $dates
+                data\$metadata\$$col <- as_datetime(data\$metadata\$$col)
+            #end for
+            saveRDS(data, "$ampvis")
+            @SAVE_METADATA_LIST@
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="rds_metadata_input_macro" metadata_optional="false"/>
+        <expand macro="metadata_select" an="name" argument="character" multiple="true" label="Character metadata variables">
+        </expand>
+        <expand macro="metadata_select" an="name" argument="numbers" multiple="true" label="Numerical metadata variables">
+            <filter type="param_value" column="0" ref="character" keep="false"/>
+        </expand>
+        <expand macro="metadata_select" an="name" argument="integers" multiple="true" label="Discrete numerical metadata variables (integers)">
+            <filter type="param_value" column="0" ref="character" keep="false"/>
+            <filter type="param_value" column="0" ref="numbers" keep="false"/>
+        </expand>
+        <expand macro="metadata_select" an="name" argument="dates" multiple="true" label="Date metadata variables">
+            <filter type="param_value" column="0" ref="character" keep="false"/>
+            <filter type="param_value" column="0" ref="numbers" keep="false"/>
+            <filter type="param_value" column="0" ref="integers" keep="false"/>
+        </expand>
+    </inputs>
+    <outputs>
+        <data name="ampvis" format="ampvis2"/>
+        <data name="metadata_list_out" format="tabular" label="${tool.name} on ${on_string}: metadata list"/>
+    </outputs>
+    <tests>
+        <!-- -->
+        <test expect_num_outputs="2">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
+            <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
+            <param name="numbers" value="Year"/>
+            <param name="dates" value="Date"/>
+            <output name="ampvis" ftype="ampvis2">
+                <assert_contents>
+                    <has_size value="11966" delta="1000"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+What it does
+============
+
+Allows to manually set the data types of metadata. `ampvis2: load` tries to
+detect the metadata data types automatically. If this is not as desired
+the data types can be set manually with this tool.
+
+Input
+=====
+
+@HELP_RDS_INPUT@
+
+@HELP_METADATA_LIST_INPUT@
+
+Output
+======
+
+**RDS**
+
+The main output of the tool is an RDS data set that contains the R representation of
+the ampvis2 object containing the same data as the input, but with data types changes
+as chosen in the input form.
+
+**Metadata list file**
+
+Updated metadata (only column 4 should change and reflect the desired datatype changes).
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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